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1. Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres

   https://doi.org/10.1128/mSphere.00035-20  

   Bledsoe, Regina B. ; Goodwillie, Carol ; Peralta, Ariane L. ( June 2020 , mSphere)

   Campbell, Barbara J. (Ed.)

   ABSTRACT In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C 3 forb, C 4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilizationmore »serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling. IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways.« less
2. Glucocorticoids coordinate changes in gut microbiome composition in wild North American red squirrels

   https://doi.org/10.1038/s41598-022-06359-5  

   Petrullo, Lauren ; Ren, Tiantian ; Wu, Martin ; Boonstra, Rudy ; Palme, Rupert ; Boutin, Stan ; McAdam, Andrew G. ; Dantzer, Ben ( February 2022 , Scientific Reports)

   The gut microbiome impacts host health and fitness, in part through the diversification of gut metabolic function and pathogen protection. Elevations in glucocorticoids (GCs) appear to reduce gut microbiome diversity in experimental studies, suggesting that a loss of microbial diversity may be a negative consequence of increased GCs. However, given that ecological factors like food availability and population density may independently influence both GCs and microbial diversity, understanding how these factors structure the GC-microbiome relationship is crucial to interpreting its significance in wild populations. Here, we used an ecological framework to investigate the relationship between GCs and gut microbiome diversity in wild North American red squirrels (Tamiasciurus hudsonicus). As expected, higher GCs predicted lower gut microbiome diversity and an increase in metabolic taxa. Surprisingly, but in line with prior empirical studies on wild animals, gastrointestinal pathogens decreased as GCs increased. Both dietary heterogeneity and an upcoming food pulse exhibited direct effects on gut microbiome diversity, whereas conspecific density and reproductive activity impacted diversity indirectly via changes in host GCs. Our results provide evidence of a gut–brain axis in wild red squirrels and highlight the importance of situating the GC-gut microbiome relationship within an ecological framework.
3. Effect of Pepper-Containing Diets on the Diversity and Composition of Gut Microbiome of Drosophila melanogaster

   https://doi.org/10.3390/ijms21030945  

   Garcia-Lozano, Marleny ; Haynes, Joshua ; Lopez-Ortiz, Carlos ; Natarajan, Purushothaman ; Peña-Garcia, Yadira ; Nimmakayala, Padma ; Stommel, John ; Alaparthi, Suresh B. ; Sirbu, Cristian ; Balagurusamy, Nagamani ; et al ( February 2020 , International Journal of Molecular Sciences)

   One of the greatest impacts on the gastrointestinal microbiome is diet because the host and microbiome share the same food source. In addition, the effect of diet can diverge depending on the host genotype. Diets supplemented with phytochemicals found in peppers might cause shifts in the microbiome. Thus, understanding how these interactions occur can reveal potential health implications associated with such changes. This study aims to explore the gut microbiome of different Drosophila genetic backgrounds and the effects of dietary pepper treatments on its composition and structure. We analyzed the gut microbiomes of three Drosophila melanogaster genetic backgrounds (Canton-S, Oregon-RC, and Berlin-K) reared on control and pepper-containing diets (bell, serrano, and habanero peppers). Results of 16S rRNA gene sequencing revealed that the variability of Drosophila gut microbiome can be driven mainly by genetic factors. When the abundance of these communities is considered, pepper-containing diets also appear to have an effect. The most relevant change in microbial composition was the increment of Lactobacillaceae and Acetobacteraceae abundance in the pepper-containing diets in comparison with the controls in Oregon-RC and Berlin-K. Regression analysis demonstrated that this enhancement was associated with the content of phenolic compounds and carotenoids of the peppers utilized in thismore »study; specifically, to the concentration of β-carotene, β-cryptoxanthin, myricetin, quercetin, and apigenin.« less
4. Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study

   https://doi.org/10.1128/msystems.00965-22  

   Rojas, Connie A. ; Holekamp, Kay E. ; Viladomat Jasso, Mariette ; Souza, Valeria ; Eisen, Jonathan A. ; Theis, Kevin R. ( January 2022 , mSystems)

   Hird, Sarah M. (Ed.)

   The gut microbiome provides vital functions for mammalian hosts, yet research on its variability and function across adult life spans and multiple generations is limited in large mammalian carnivores. Here, we used 16S rRNA gene and metagenomic high-throughput sequencing to profile the bacterial taxonomic composition, genomic diversity, and metabolic function of fecal samples collected from 12 wild spotted hyenas ( Crocuta crocuta ) residing in the Masai Mara National Reserve, Kenya, over a 23-year period spanning three generations. The metagenomic data came from four of these hyenas and spanned two 2-year periods. With these data, we determined the extent to which host factors predicted variation in the gut microbiome and identified the core microbes present in the guts of hyenas. We also investigated novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition varied temporally, but despite this, a core set of 14 bacterial genera were identified. The strongest predictors of the microbiome were host identity and age, suggesting that hyenas possess individualized microbiomes and that these may change with age during adulthood. The gut microbiome functional profiles of the four adult hyenas were also individual specificmore »and were associated with prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyenas’ guts; some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species-level matches to genomes in existing reference databases. IMPORTANCE There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host’s life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores, and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores, but over 80% of MAGs were novel and from species not previously represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of nonmodel wild hosts, using multiple sequencing methods and computational approaches and at distinct scales of analysis.« less
5. Gut Microbiome: Profound Implications for Diet and Disease

   https://doi.org/10.3390/nu11071613  

   Hills, Ronald D. ; Pontefract, Benjamin A. ; Mishcon, Hillary R. ; Black, Cody A. ; Sutton, Steven C. ; Theberge, Cory R. ( July 2019 , Nutrients)

   The gut microbiome plays an important role in human health and influences the development of chronic diseases ranging from metabolic disease to gastrointestinal disorders and colorectal cancer. Of increasing prevalence in Western societies, these conditions carry a high burden of care. Dietary patterns and environmental factors have a profound effect on shaping gut microbiota in real time. Diverse populations of intestinal bacteria mediate their beneficial effects through the fermentation of dietary fiber to produce short-chain fatty acids, endogenous signals with important roles in lipid homeostasis and reducing inflammation. Recent progress shows that an individual’s starting microbial profile is a key determinant in predicting their response to intervention with live probiotics. The gut microbiota is complex and challenging to characterize. Enterotypes have been proposed using metrics such as alpha species diversity, the ratio of Firmicutes to Bacteroidetes phyla, and the relative abundance of beneficial genera (e.g., Bifidobacterium, Akkermansia) versus facultative anaerobes (E. coli), pro-inflammatory Ruminococcus, or nonbacterial microbes. Microbiota composition and relative populations of bacterial species are linked to physiologic health along different axes. We review the role of diet quality, carbohydrate intake, fermentable FODMAPs, and prebiotic fiber in maintaining healthy gut flora. The implications are discussed for various conditions includingmore »obesity, diabetes, irritable bowel syndrome, inflammatory bowel disease, depression, and cardiovascular disease.« less